Olga Kharlan, a four-time Olympic medallist, beat the officially-neutral Russian Anna Smirnova, but after the match was over offered to tap swords rather than the traditional handshake.
Touching blades was used as an alternative to handshakes at fencing competitions during the coronavirus pandemic.
After Kharlan rebuffed Smirnova the Russian refused to leave after the bout for more than 50 minutes, sitting on a chair on the fencing piste in an apparent protest at her opponent's behaviour.
Kharlan was later listed as excluded from the event in the tournament bracket.
The International Fencing Federation has not yet commented on the reason.
Smirnova was not reinstated and Bulgarian fencer Yoana Ilieva, who Kharlan had been due to face next, advanced by walkover.
Another Ukrainian, Igor Reizlin, withdrew from his event at the same world championships when he was drawn to compete against a Russian in the men's epee tournament on Wednesday before the decree was published.
Earlier this week Ukraine's government lifted its ban on athletes competing against Russians as long as they are listed as neutral athletes.
The move was welcomed by the International Olympic Committee (IOC) as competitors begin qualifying for next year's games in Paris.
The IOC said: "We are glad that they will be given this opportunity, and at the same time we are aware of the difficult inner conflicts they may have, given the aggression against their country."
"Therefore, we encourage international federations to handle situations involving Ukrainian and Individual Neutral Athletes with the necessary degree of sensitivity. We continue to stand in full solidarity with the Ukrainian athletes and the Olympic community of Ukraine."
The IOC - which initially recommended that sports bodies exclude Russian and Belarusian athletes on safety grounds last year - says it has not taken a final decision on allowing "neutral" Russian and Belarusian athletes at next year's Paris Olympics.
Ukraine had previously objected strongly to the policy, with President Volodymyr Zelenskyy saying in January that "any neutral flag of Russian athletes is stained with blood" and that Russia would exploit their presence for propaganda.
Ukrainian teams in fencing and judo already boycotted events which included Russians following last year's full-scale invasion of Ukraine.
IOC president Thomas Bach, who has signalled his organisation will monitor the behaviour of Russians and Belarusians given neutral status, is himself a former fencer who won a gold medal at the 1976 Montreal Olympics.
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